Thursday, November 23, 2006

Bill Dembski Needs Help, Again

I suspect that the “junk DNA” hypothesis was originally made on explicitly Darwinian grounds. Can someone provide chapter and verse? Clearly, in the absence of the Darwinian interpretation, the default assumption would have been that repetitive nucleotide sequences must have some unknown function.

Fortunately, there are some smart people who post comments on Uncommon Descent. They have told Bill that the concept of junk DNA is explicitly non-Darwinian. It was proposed by scientists who didn't feel the need to explain everything as an adaptation.

I don't know how many times we've explained to Bill that not all evolutionary biologists are "Darwinists." I know I first told him four years ago but I'm sure there were others before me. He seems to be a very slow learner.

One of these years he'll realize that there's more to evolution than just natural selection.

9 comments
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Questions (including the origin of the misnomer "junk") about the Zeitgeist of 21st Century ("Junk DNA") should be welcome.

Why not focus directly on the strictly scientific question of revealing its function?

While there are plenty of science issues at http://www.junkdna.comthe most recent breakthrough (23rd of November) on diversity of human genome is a particulary pertinent "debate issue"; e.g. how the 98.7% of human Genome is responsible for the enormous human diversity - when 99.9% or our Genes are identical (and only the "beyond Genes" regions might determine our diversity).

In genetic programing simulation runs with variable length genomes, junk "genes" will inevitably accumulate, often taking over 90% of the genome. It's an evolved defense against the destructive effects of the crossover operator. I've read that this may also be one reason behind junk dna (and introns) in biology. If true, it would be an adaptive "Darwinian" explanation - one which does not derive from the phenotype of the individual, but rather the stability of its offspring.

It's an evolved defense against the destructive effects of the crossover operator.

What does that mean? Homologous recombination isn't destructive (unless it makes a rare mistake).

I've read that this may also be one reason behind junk dna (and introns) in biology. If true, it would be an adaptive "Darwinian" explanation - one which does not derive from the phenotype of the individual, but rather the stability of its offspring.

This doesn't work as an explanation. I think it's based on faulty logic but you'll have to explain that "logic" in order for me to make a better judgement.

The yeast Saccharomyces cerevisiae has a high rate of homologous recombination but almost no junk DNA. Is that consistent with your explanation?

What does that mean? Homologous recombination isn't destructive (unless it makes a rare mistake).

In genetic programming models, the crossover operator (even though it increases variation) has the adverse effect of breaking up useful functional "groups" of software "genes", that work together. The accumulation of junk genes in the genome increases the probability that crossover will occur in groups of those junk genes and decreases the probability that working functional groups will be broken up. Thus genomes with junk dna are more fit (for the offspring). In GP, junk gene sequenes are called "introns", and GP crossover is usually not "homologous" to start out with. One book that discusses all this is Genetic Programming, an Introduction, by Banzhaf et al

Yeah, I don't know if this would be a significant problem in biology for homologous recombination (they're not exactly homologous) but the wiki seems to think so (third bullet under hypothesis and origin):http://en.wikipedia.org/wiki/Junk_DNA.Perhaps there was time when crossover was less homologous.

The yeast Saccharomyces cerevisiae has a high rate of homologous recombination but almost no junk DNA. Is that consistent with your explanation?

No it isn't. But I'm not suggesting that recombination is a sole cause. just a contributing cause, based on what I've seen in GP. If you could show that asexual organisms had huge amounts of junk dna, that would work against me as well.

jeffw says,No it isn't. But I'm not suggesting that recombination is a sole cause. just a contributing cause, based on what I've seen in GP.

It's very dangerous to draw conclusions about real biology from genetic programming. The algorithms in genetic programming are not good models of biological evolution.

The Wikipedia article lists several speculations about possible functions of junk DNA. (If any of them are correct then the DNA isn't junk.)

The one you're referring to is ..

Junk DNA may act as a protective buffer against genetic damage and harmful mutations. For example, a high proportion of nonfunctional sequence makes it unlikely that a functional element will be destroyed in a chromosomal crossover event, possibly making a species more tolerant to this important mechanism of genetic recombination.

This isn't a serious contender. Extra DNA will not protect against mutations and it will not "protect" against recombination since recombination is not destructive.

Furthermore, there's no way such protection against future events could evolve by natural selection. Evolution doesn't see into the future.

It's very dangerous to draw conclusions about real biology from genetic programming.

Agreed.

it will not "protect" against recombination since recombination is not destructive.

As a non-biologist, I'm not sure what to make of this. I've seen conflicting descriptions of recombination. Some of them say it leaves genes alone, and some say it can happen within a gene (If I remember right, The Selfish Gene says this). I even remember reading that it can happen within introns, so that function protein groups are preserved.

Furthermore, there's no way such protection against future events could evolve by natural selection. Evolution doesn't see into the future.

It most certainly does in GP, when crossover is destructive and the genome is of variable length.

...One more point: for this model to be meaningful, it doesn't have to be "destructive" in the sense that it breaks up a gene (cistron), just that it breaks up a functional group of genes working together (for homologous crossover, I don't know what that would mean).

In any case, here's the Selfish Gene reference: pg 28, 30th anniversary edition: "..some people use the word gene interchangeably with cistron. But crossing-over does not respect boundaries between cistrons. Splits may occur within cistrons as well as between them."

"It's very dangerous to draw conclusions about real biology from genetic programming. The algorithms in genetic programming are not good models of biological evolution."I see an out of context quotemine being snagged up in a hurry.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.